Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
 
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
  
 +
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
  
== October 3, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_November_2019|November]]
  
=== SObA comparison graphs ===
 
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
 
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
 
** [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1 Example comparison between lin-3 and let-23]
 
* [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
 
** [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1) Example comparison between lin-3 and let-23]
 
* What information does a user most care about?
 
# What terms (nodes) are annotated to gene 1 and what terms to gene 2
 
# For a given term, what is the relative number of annotations between gene 1 and gene 2.
 
# For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
 
* # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
 
* Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
 
* In either case users need a good legend and/or documentation
 
* Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes
 
  
=== Germ line discussion ===
+
== December 5, 2019 ==
* Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
 
* Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
 
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
 
* Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)
 
  
=== Script to remove blank entries from Postgres ===
+
=== New interaction Venn diagram tool ===
* Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
+
* [https://staging.wormbase.org/species/c_elegans/gene/WBGene00000912#08--10 daf-16 interactions]
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
+
* Venn diagram shows how various interactors have multiple interaction types with a common focus gene
* Does anyone object to removing these entries throughout Postgres?
+
* For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
* Juancarlos will remove all the empty fields identified by his script
+
* Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
 +
* Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
 +
* Request: could there be a toggle to include/exclude high-throughput interactions?
 +
* Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
 +
* Request: Change the wording "Browse selection" to something like "View/analyze gene list"
 +
* Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?
  
 +
=== New round of phenotype requests ===
 +
* GMail really throttling email sending
 +
* Chris will reach out to Google/GMail to see if we can:
 +
** A) get a clear explanation about what their restrictions are and how they work and
 +
** B) see if we can get a paid plan to help expedite the email process (see how much cost)
  
== October 10, 2019 ==
+
=== Aligning interaction data with GO and GO-CAM ===
 +
* The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
 +
* Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
 +
* Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
 +
** Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
 +
* Chris and Kimberly will meet to discuss further
  
=== Biocuration 2020 ===
+
=== Short SObA talk at Alliance meeting ===
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
+
* Raymond prepared to give short talk on SObA to the Alliance group
* Dates: Sunday May 17th to Wednesday May 20th, 2020
 
* Will have 3rd POTATO workshop
 
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
 
* Key Dates
 
** October 31, 2019 - Paper Submission Deadline
 
** January 24, 2020 - Abstract  and Workshop Submission Deadline
 
** March 6, 2020 - Notification of Acceptance
 
** April 6, 2020 - Early Bird Registration Ends
 
** May 8, 2020 - Registration Deadline
 
* Academic ISB Member, early bird registration fee is $250
 
* Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference
 
  
=== ICBO 2020 ===
+
=== Single cell data visualization tool ===
* International Conference on Biomedical Ontologies
+
* Eduardo will present to Paul's lab meeting tomorrow
* [https://icbo2020.inf.unibz.it/ Meeting website]
+
* Will discuss at Alliance expression working group pre-meeting
* Held in Bozen-Bolzano, Italy
 
* 16 - 19 September 2020
 
 
 
=== SObA comparison tool ===
 
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
 
 
 
=== Textpresso derived paper connections ===
 
* For example for strains and constructs, maybe anatomy terms?
 
* May want to flag Textpresso predictions (as opposed to manually connected)
 
* Couple of options:
 
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
 
** 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
 
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
 
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
 
** 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
 
* Transgene pipeline:
 
** Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
 
** Another script, captures Ex transgenes as well, automatically connects to construct objects
 
** WB only displays verified papers; unverified (predicted) associations are not dumped
 
* Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
 
* Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
 
* Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
 
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities
 
 
 
 
 
== October 17, 2019 ==
 
 
 
=== Alliance All Hands Face-to-Face ===
 
* Flights: has everyone already booked? No, not yet
 
* Any coordination of flights from Pasadena/LA?
 
** Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings
 
 
 
=== SObA Comparison Tool ===
 
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
 
* Prototype discussed last week, updated with feedback from prior discussions
 
* Would this be a stand-alone tool discoverable under the Tools menu?
 
** Possibly; could be a gene page widget, but may be out of place
 
** Stand-alone tool probably makes more sense
 
* Life stage graph doesn't specify expression pattern vs. expression cluster; pretty much only expression patterns (no clusters)
 
 
 
=== SObA ===
 
* Raymond intending to share progress on SObA at December Alliance All-Hands Face-to-Face
 
* For example, share GO SObA graph for other species
 
* Will need to be dependent on a SOLR server with all species data
 
** Raymond has run into problems trying to setup his own SOLR server
 
** Raymond asked Seth Carbon if we could us GO server, but he prefers not
 
** Appear to be software versioning issues, possible memory issues
 
 
 
=== GO meeting ===
 
* Kimberly can give update on recent updates to GO from the recent GO meeting
 
* Slides are shared online
 
 
 
=== "all stages Ce" life stage ===
 
* Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
 
* "all stages Ce" is currently the root node of the C. elegans branch, but needs to change to generic "C. elegans life stage"
 
* Should we:
 
** 1) Create a "C. elegans life span" or "C. elegans life cycle" term to represent the entire life span and annotate to that?
 
*** Does this mean that, for example, a gene is expressed at some point during the life cycle or consistently throughout the entire life span?
 
** 2) Annotate instead to, for example, "embryo Ce", "larva Ce", and "adult Ce" individually
 
* Note: authors are often vague in their descriptions simply saying "during all stages" possibly stating a beginning and end of the range
 
* Wen: not comfortable making a decision right now; want to discuss with Gary Williams and with other MOD members about how to handle large scale expression data
 
* Daniela: will look through existing (old and new) expression pattern annotations made to "all stages Ce" to see if it would be reasonable to annotate each case individually to "embryo Ce", "larva Ce", and "adult Ce" individually
 
 
 
=== Gene class missing description ===
 
* The gene class "aatf" has no description, so in the aatf-1 gene page Overview widget, the gene has empty parentheses next to the gene name where there should be a description of what "aatf" stands for (coming from the ?Gene_class description)
 
* Jae or Ranjana will create a ticket and assign it to someone at Hinxton
 
 
 
 
 
== October 24, 2019 ==
 
 
 
=== Textpresso links from WB page References widgets ===
 
* Discussed with Sibyl and Adam on last week's Textpresso call
 
* Sibyl working on mockups for including Textpresso derived paper associations in the References widget
 
* Had originally considered for the following classes
 
** Strain
 
** Gene
 
** Variation
 
** Transgene
 
** Construct
 
** Anatomy_term
 
* Sibyl asks: could we put this link in all References widgets in WB?
 
** Classes with References widgets include:
 
*** Antibody
 
*** Clone
 
*** Construct
 
*** Expression cluster
 
*** Expression pattern
 
*** Gene
 
*** Interaction
 
*** Life stage
 
*** Rearrangement
 
*** RNAi
 
*** Strain
 
*** Transgene
 
*** Variation
 
*** Analysis
 
*** Molecule
 
*** Process
 
** Any Textpresso search on internal WB identifiers, like WBInteraction000###### or WBRNAi00######, or on long complicated names is certainly meaningless, so the following classes are probably ruled out:
 
*** Antibody
 
*** Expression cluster
 
*** Expression pattern
 
*** Interaction
 
*** RNAi
 
*** Analysis
 
** Otherwise it could probably be beneficial to include the additional classes, searching on public name:
 
*** Clone
 
*** Life stage
 
*** Rearrangement
 
*** Molecule
 
*** Process
 
* Created Google Doc summary [https://docs.google.com/document/d/19y5wNIHLmBRm4z7Rz6NG-NQYlZbtobXuQcH6dz0s8Rg/edit?usp=sharing here]
 
* So the current list of candidate classes is:
 
** Strain
 
** Gene
 
** Variation
 
** Transgene
 
** Construct
 
** Anatomy_term (no References widget currently)
 
** Clone
 
** Life stage
 
** Rearrangement
 
** Molecule
 
** Process
 
* Eventually, we may want to incorporate papers found by Textpresso directly into the References widget
 
** We would want predicted associations to be made explicitly so
 
** We could populate the database, but there are reservations about doing this
 
 
 
 
 
=== Updates from GOC Meeting, Berkeley ===
 
* Status of MOD Imports into Noctua
 
** Starting with WormBase and MGI GO annotations into GO-CAM
 
** GPAD/GPI is standard import format
 
* GO-CAM Specifications and Validation
 
* Noctua Form
 
* Pathways2GO
 
* Priorities for next 6 months:
 
** Create gene-centric Noctua views
 
** Create pathway-centric Noctua views
 
 
 
 
 
== October 31, 2019 ==
 
 
 
=== ?Genotype class ===
 
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
 
* Several classes have a "Genotype" tag with text entry
 
** Strain
 
** 2_point_data
 
** Pos_neg_data
 
** Multi_pt_data
 
** RNAi
 
** Phenotype_info
 
** Mass_spec_experiment (no data as of WS273)
 
** Condition
 
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
 
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
 
** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
 
** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
 
** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
 
** Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
 
** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
 
** Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
 
** Reference to parent strain, like "Parent strain is AG359"
 
** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
 
** Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)"
 

Latest revision as of 21:08, 5 December 2019

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December 5, 2019

New interaction Venn diagram tool

  • daf-16 interactions
  • Venn diagram shows how various interactors have multiple interaction types with a common focus gene
  • For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
  • Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
  • Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
  • Request: could there be a toggle to include/exclude high-throughput interactions?
  • Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
  • Request: Change the wording "Browse selection" to something like "View/analyze gene list"
  • Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?

New round of phenotype requests

  • GMail really throttling email sending
  • Chris will reach out to Google/GMail to see if we can:
    • A) get a clear explanation about what their restrictions are and how they work and
    • B) see if we can get a paid plan to help expedite the email process (see how much cost)

Aligning interaction data with GO and GO-CAM

  • The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
  • Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
  • Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
    • Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
  • Chris and Kimberly will meet to discuss further

Short SObA talk at Alliance meeting

  • Raymond prepared to give short talk on SObA to the Alliance group

Single cell data visualization tool

  • Eduardo will present to Paul's lab meeting tomorrow
  • Will discuss at Alliance expression working group pre-meeting